Question: Pindel installation failing due to htslib
0
gravatar for cdastmalchi
5 days ago by
cdastmalchi0 wrote:

I have made the following Dockerfile to install pindel:

# Use Python base image from DockerHub
FROM python:2.7

RUN apt-get update && apt-get install -y \
  bzip2 \
  wget \
  make \
  ncurses-dev \
  zlib1g-dev \
  g++ \
  python-pip \
  git \
  gcc \
  liblzma-dev

RUN pip install awscli boto3

# Install htslib
WORKDIR /usr/bin
RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 \
    && tar -vxjf htslib-1.9.tar.bz2 \
    && cd htslib-1.9 \
    && make

# Install pindel
WORKDIR /usr/bin
RUN git clone git://github.com/genome/pindel.git \
    && cd pindel \
    && ./INSTALL /usr/bin/htslib-1.9/

ENV PATH="/usr/bin/:$PATH"

However, when I try building this image, I get errors such as:

   ^~~
make[1]: Leaving directory '/usr/bin/pindel/src'
make[1]: *** [Makefile:47: pindel.o] Error 1
make: *** [Makefile:12: pindel] Error 2

INSTALL failed
Possible reasons: 
1. 'cannot cd to [path]
->the htslib path provided was incorrect

2. 'cannot find -lbam'
->htslib was not properly compiled/made, in that case, go to the htslib directory and follow the htslib installation instructions
and run 'make'.

or

compilation terminated.
In file included from output_sorter.cpp:27:
pindel.h:34:10: fatal error: htslib/khash.h: No such file or directory
 #include "htslib/khash.h"
          ^~~~~~~~~~~~~~~~
compilation terminated.
In file included from reporter.h:27,
                 from search_tandem_duplications_nt.cpp:23:
pindel.h:34:10: fatal error: htslib/khash.h: No such file or directory
 #include "htslib/khash.h"
          ^~~~~~~~~~~~~~~~
compilation terminated.
In file included from reporter.h:27,
                 from search_tandem_duplications.cpp:23:
pindel.h:34:10: fatal error: htslib/khash.h: No such file or directory
 #include "htslib/khash.h"
          ^~~~~~~~~~~~~~~~

I have tried installing both htslib and samtools and referring to those directories in my ./INSTALL ... command, but nothing is working! I even tried walking through these installation steps manually on an Amazon instance and get the following error:

mv: cannot stat ‘src/pindel’: No such file or directory
mv: cannot stat ‘src/pindel2vcf’: No such file or directory
mv: cannot stat ‘src/sam2pindel’: No such file or directory
mv: cannot stat ‘src/pindel2vcf4tcga’: No such file or directory

Help would be much appreciated :)

pindel docker htslib • 74 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by cdastmalchi0
0
gravatar for Mensur Dlakic
5 days ago by
Mensur Dlakic2.4k
USA
Mensur Dlakic2.4k wrote:

If I understand this script correctly, it is trying to download, compile, and install in WORKDIR /usr/bin. First, I think that's a terrible idea to begin with, at least for downloading and compiling. Second, don't think this script can be executed in /usr/bin without root privileges.

I would suggest manually cloning both programs in a different directory from /usr/bin and compiling them one by one. Simply copy/paste the commands from the script.

ADD COMMENTlink written 5 days ago by Mensur Dlakic2.4k

Thank you. I have already tried using other directories in the script besides /usr/bin for downloading and compiling, however I still get the same error. And the whole point of using a Docker container is to bypass any "manual" steps; I'm trying to use this Pindel program as part of a bioinformatics pipeline.

ADD REPLYlink modified 5 days ago • written 5 days ago by cdastmalchi0
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